from the urls-we-dig-up dept

Astrobiology is a field that doesn't have a whole lot of experimental evidence, but it's interesting to entertain the possibilities of life that might exist elsewhere in the universe. So far, we've been looking for ET biology that's similar to our own, but there's nothing that says biology must be based on DNA/RNA/proteins/etc. Here are just a few more links on possibly finding life on other worlds.

from the urls-we-dig-up dept

Your fate is not completely written in your DNA. Environmental conditions can certainly change your life significantly, and you can even control some risk factors to your benefit. Sure, some things like poverty aren't quite under anyone's direct control (and it has a measurable detrimental effect on kids' DNA). But if you're looking for some more good reasons to make a new year's resolution, maybe think about how you can change your epigenetics for the better?

Exercise apparently changes how genes are expressed. The field of epigenetics isn't well understood yet, but there are a lot of factors that can change how our genes send signals to our bodies. By studying people riding a stationary bicycle using only one leg, researchers could find evidence of genetic differences in the muscles of legs that exercised and that did not. [url]

an invention that may be the most important new genetic engineering technique since the beginning of the biotechnology age in the 1970s. The CRISPR system, dubbed a "search and replace function" for DNA, lets scientists easily disable genes or change their function by replacing DNA letters. During the last few months, scientists have shown that it's possible to use CRISPR to rid mice of muscular dystrophy, cure them of a rare liver disease, make human cells immune to HIV, and genetically modify monkeys.

Unfortunately, rivalry between scientists claiming the credit for key parts of CRISPR threatens to spill over into patent litigation:

[A researcher at the MIT-Harvard Broad Institute, Feng] Zhang cofounded Editas Medicine, and this week the startup announced that it had licensed his patent from the Broad Institute. But Editas doesn't have CRISPR sewn up. That's because [Jennifer] Doudna, a structural biologist at the University of California, Berkeley, was a cofounder of Editas, too. And since Zhang's patent came out, she's broken off with the company, and her intellectual property -- in the form of her own pending patent -- has been licensed to Intellia, a competing startup unveiled only last month. Making matters still more complicated, [another CRISPR researcher, Emmanuelle] Charpentier sold her own rights in the same patent application to CRISPR Therapeutics.

Things are moving quickly on the patent front, not least because the Broad Institute paid extra to speed up its application, conscious of the high stakes at play here:

Along with the patent came more than 1,000 pages of documents. According to Zhang, Doudna's predictions in her own earlier patent application that her discovery would work in humans was "mere conjecture" and that, instead, he was the first to show it, in a separate and "surprising" act of invention.

The patent documents have caused consternation. The scientific literature shows that several scientists managed to get CRISPR to work in human cells. In fact, its easy reproducibility in different organisms is the technology's most exciting hallmark. That would suggest that, in patent terms, it was "obvious" that CRISPR would work in human cells, and that Zhang's invention might not be worthy of its own patent.

Whether obvious or not, it looks like the patent granted may complicate turning the undoubtedly important CRISPR technique into products. That, in its turn, will mean delays for life-changing and even life-saving therapies: for example, CRISPR could potentially allow the defective gene that causes serious problems for those with cystic fibrosis to be edited to produce normal proteins, thus eliminating those problems.

Although supporters of patents will argue as usual that they are necessary to encourage the discovery of new treatments, CRISPR is another example where patents simply get in the way. The discoveries were made by scientists in the course of their work in fundamental science at academic institutions, not because they were employed by a company to come up with a new product. According to some, the basic application of CRISPR to human cells that everyone is fighting over may even be obvious. The possibility of legal action will doubtless discourage investment in companies working in this area, and thus slow down the flow of new treatments. As usual, the only ones who win here are the lawyers.

from the now-go-forth-and-innovate dept

Back in 2013, the Supreme Court struck down patents that Myriad Genetics had obtained on naturally-occuring DNA sequences linked to breast cancer. As a result of that judgment, other companies started offering diagnostic tests based on the genes in question. Myriad claimed that despite losing patents on the DNA, its patents on tests based on that DNA were still valid, and took legal action to stop others from offering similar services. As we reported earlier this year, a federal district court judge refused to grant Myriad a preliminary injunction against one of those new entrants, and now the genetic testing patents have been ruled invalid, as Bloomberg reports:

Myriad Genetics Inc. (MYGN) can't block competitors' DNA tests to determine risk for breast and ovarian cancer after a U.S. appeals court said three patents on the tests never should have been issued.

The patents cover products of nature and ideas that aren't eligible for legal protection, the U.S. Court of Appeals for the Federal Circuit said in an opinion posted today on the court's docket. The court upheld a trial judge's decision to allow the competing tests, including those made by Ambry Genetics Corp., to remain on the market.

That's great news for women who can now choose freely from among a range of diagnostic options, often at prices substantially less than comparable testing offered by Myriad. It means that Myriad's monopoly on data derived from those tests has been broken: thanks to its patents, it has created the world's largest database of mutations in breast cancer genes. Most importantly, perhaps, it opens up the field of gene-based diagnostic testing to allow new entrants to experiment and innovate more freely. That, rather than granting monopolies to a few companies, is far more likely to lead to new medical breakthroughs, products and services.

from the urls-we-dig-up dept

The classic question of "which came first: the chicken or the egg?" is not that easy to answer. There are a lot of unanswered (and perhaps unanswerable) questions about the origins of life. What came first: DNA, RNA or proteins? How did chirality start? We have a few clues, but without a time machine, we can't quite observe what actually happened. Here are just a few scientific probes that could help us understand the early stages of our biosphere.

from the matter-of-life-and-death dept

It's taken a surprisingly long time for countries to settle the question of whether something as fundamental as genes can be patented or not. And opinions still differ: last year, the US Supreme Court ruled that naturally-occurring genes couldn't be patented, while more recently, Australia went the other way (although it's possible that ruling could be overturned by higher courts there). Now a test case has been filed this week to establish the situation in Canada, as the Toronto Star reports:

Monday's legal case, brought by the Children's Hospital of Eastern Ontario (CHEO), deals with five patents held in Canada by the University of Utah on genes and tests for an inherited cardiac condition called Long QT syndrome.

Interestingly, the case is not about genes that play a role in developing breast cancer, which were the focus of attention in both the US and Australian court decisions. However, as with breast cancer, the effects of allowing gene patents in this area is the same -- to drive up the cost of testing:

The two-tier test [for Long QT syndrome] currently costs approximately $4,500 (U.S.) per person, CHEO estimates, whereas researchers at the hospital believe they could administer the same process in-house for about half the cost.

"The collective impact (of this case) could easily be in the orders of millions of dollars for the healthcare system," said Gail Graham, a clinical geneticist at the hospital.

This isn't just about money: it's a matter of life and death. The more expensive a gene-based test, the less likely it will be used by hospitals, which are struggling to make their limited budgets stretch as far as possible. And that means that medical conditions will be missed, with serious, possibly fatal, consequences.

from the because-DNA-is-digital-data dept

When the first human genome was sequenced -- that is, when most of the 3 billion base-pairs that go to make up our DNA were elucidated -- as part of the Human Genome Project, around $3 billion was spent. Today, the cost of sequencing is falling even faster than Moore's Law, which means everyone could have their genome sequenced soon, if they wished (and maybe even if they don't....). By analyzing the DNA, and looking at the gene variants found there, it is possible to spot predispositions to certain diseases or medical conditions, potentially allowing lifestyle changes or treatment that reduce the risk. The well-known personal genomics company 23andMe was offering this kind of service, at least on a small scale. But that stopped at the end of last year, as the company explains:

We no longer offer our health-related genetic reports to new customers to comply with the U.S. Food and Drug Administration's directive to discontinue new consumer access during our regulatory review process.

At this time, we do not know the timeline as to which health reports might be available in the future or when they might be available.

in November 2013, the Food and Drug Administration had cracked down on 23andMe. The direct-to-consumer gene testing company's popular DNA health reports and slick TV ads were illegal, it said, since they'd never been cleared by the agency.

But as that same article goes on to explain in detail, users of 23andMe are having no difficulty in getting around that ban on obtaining health-related analyses of their genomes, using third-party sites like Promethease:

Promethease was created by a tiny, two-man company run as a side project by Greg Lennon, a geneticist based in Maryland, and Mike Cariaso, a computer programmer. It works by comparing a person's DNA data with entries in SNPedia, a sprawling public wiki on human genetics that the pair created eight years ago and run with the help of a few dozen volunteer editors. Lennon says Promethease is being used to build as many as 500 gene reports a day.

That kind of analysis is possible because, once sequenced, DNA is essentially just digital data: very easy to upload and compare against biomedical databases storing information as digital files. Even though they are not currently allowed to analyze it, companies like 23andMe still provide customers with access to the raw genomic data, which can then be sent to services like Promethease for a basic report drawing on its DNA database.

This raises an interesting question: given that the information on SNPedia is drawn from public databases, can the FDA stop people using it to circumvent the ban on 23andMe? According to MIT Technology Review, the FDA believes the answers is "yes", but that just won't work in practice. Even if the FDA manages to shut down all the services like Promethease, it would be easy to write a program that searches the main public biomedical databases for exactly the same kind of information about particular gene variants found in somebody's genome. The software could be shared freely as open source, making it impossible to prevent people from obtaining the program and carrying out such searches independently on their own computers.

It's true that there are good reasons why the FDA might be concerned about members of the public being given medical analyses of their genome in inappropriate ways. For a start, the results are generally probabilistic, rather than definite predictions; that makes them hard for non-experts to interpret. And when it isn't about probabilities -- if it is certain that you will develop a disease, possibly a devastating one -- there's a strong argument that counselling needs to be made available when that information is given to the person affected.

Still, regardless of the extent to which the FDA's actions are understandable, trying to stop people comparing their DNA with publicly-available information is futile. As the copyright industry has learned the hard way, once data is digital, it is essentially uncontrollable. The best thing to do is to accept that fact and move on. In this case, that means the FDA should encourage companies offering analysis to do a good job, not block them completely.

from the to-preserve-the-integrity-of-your-precious-bodily-fluids dept

The FBI's Next Generation Identification (NGI) database has been discussed here several times, thanks to its "expeditious" blend of criminal and non-criminal data, its postponed-forever Privacy Impact Assessment the agency has been promising since 2008, the limited, four-state rollout of facial recognition software with a 20% error rate, and its peculiar exclusion of DOJ/law enforcement employees from its lifelong criminal database monitoring.

The FBI is preparing to accelerate the collection of DNA profiles for the government's massive new biometric identification database.

Developers of portable DNA analysis machines have been invited to a Nov. 13 presentation to learn about the bureau's vision for incorporating their technology into the FBI's new database.

So-called rapid DNA systems can draw up a profile in about 90 minutes.

DNA has been an integral part of criminal investigations for a number of years now and there's no question it has played an important role both in securing convictions and exonerating the falsely accused. But what the FBI is proposing is adding input from lab-in-a-box setups that return pass/fail DNA matches in a relative instant.

Rapid DNA analysis can be performed by cops in less than two hours, rather than by technicians at a scientific lab over several days. The benefit for law enforcement is that an officer can run a cheek swab on the spot or while an arrestee is in temporary custody. If there is a database match, they can then move to lock up the suspect immediately.

What used to take days in a secure, sterile lab now can apparently be accomplished in the "field" in a couple of hours. All technological improvements aside, this would appear to be a much less reliable method. Field drug testing kits have been available for years -- which utilize nothing more complex than chemical reactions -- and they've been shown to be far more unreliable than those utilizing them would have you believe. The same can most certainly be said about portable or on-site units wholly divorced from the normal constraints of a lab setting.

The government (so far) realizes this. That's why DNA obtained and analyzed by these units aren't included in the national DNA database. Only results from accredited public-sector laboratories are accepted. The companies manufacturing these devices are obviously interested in seeing this law changed. In the meantime, they've pushed for states to create their own DNA databases.

The FBI would like to see this changed as well, going so far as to issue a statement that is mostly wishful thinking.

FBI officials say their program does not impact any laws currently governing the operation of CODIS. Rapid DNA techniques in booking stations, “will simply expedite the analysis and submission of lawfully obtained samples to the state and national DNA databases,” [Ann] Todd, the FBI spokeswoman, said.

Except that it would impact laws governing CODIS… as they are today.

A legislative tweak is needed to allow DNA processed by a portable machine to be entered into the FBI's systems, bureau officials acknowledge.

Again, the FBI places efficiency above everything else. "Tweaking" the law to include portable devices would "expedite" the filling of the FBI's biometric database. Faster is better, even if the analysis method isn't as reliable as that performed by accredited labs. False positives/negatives are just the acceptable collateral damage of "combating crime and protecting the United States."

There's a huge backlog of untested DNA waiting for CODIS-qualified lab analysis. Offloading some of the work to private labs or portable devices sounds like a great way ease that congestion, but it actually could create more problems. If the government believes that only its chosen labs are capable of producing solid analysis, fixes like those suggested by three California Congressional reps would ask law enforcement (including the FBI) to decide which evidence goes the Gold Standard labs and what gets passed along to the lesser, unproven venues.

When presented with this set of options, law enforcement may prioritize cases badly, routing "time-sensitive" evidence through unproven but quicker analysis while sending out anything that can "wait" to the government's labs. Basically, without an across-the-board certification of all methods (with rigid testing and re-testing to ensure quality) as being equal, there's a good chance collected DNA will be treated just as prejudicially as the suspects themselves. And, if the expansion of CODIS inputs isn't handled with rigorous oversight, the chances of the guilty going free and the innocent being imprisoned increases.

from the urls-we-dig-up dept

The costs of analyzing DNA have come down significantly over time, so it's becoming increasingly common to sequence DNA and discover all kinds of biological curiosities. It's not quite as fast and easy as they make it look on detective shows on TV, but DNA analysis has made some pretty amazing advances. Here are just a few examples of genetic testing that you might have missed.

from the sucks-to-be-DownUnder dept

Last year, the Supreme Court made an important ruling in the Myriad Genetics case, effectively saying that genes aren't patentable, even if you can separate them out from the rest of a strand of DNA. Myriad Genetics had isolated two key genes related to breast cancer, BRCA1 and BRCA2 and argued that only it could test for those genes, because of its patent. The Supreme Court soundly rejected that, noting that you cannot patent something in nature, and clearly Myriad did not "make" the genes. Unfortunately, as we'd noted just a few months earlier, a court in Australia had come to the opposite conclusion, saying that Myriad Genetics had legitimate patents on BRCA1 and BRCA2. That case was appealed, and there was some hope that after the US's ruling, higher courts in Australia might see the light. Not yet apparently. An appeals court has agreed that genes are patentable Down Under, which means that such important genetic tests there are likely to be much more expensive and limited.

You can read the full ruling here if you'd like. The case can still be appealed to the Australian High Court, so perhaps it will take the same trajectory as in the US, where it needed the Supreme Court to finally point out the absolute insanity of patenting genes. Though, frankly, if Australia does keeps genes patentable, it might make for an interesting natural experiment to see how much innovation and research happens in both places -- one with, and one without, patents.